seqpdist: missing data vs gaps

I'm using seqpdist from the bioinformatics toolbox to calculate distance matricies for DNA alignments downloaded from ensembl. These alignments may include N's (for ambiguous data), dots for no sequence data, and dashes for gaps.

Does seqpdist recognize these notations for missing data (N and dots) and gaps (dashes) by default, or are there arguments to set this?